The theft of food aid in Yemen by Houthi rebels might be only the tip of the iceberg, officials believe, as questions multiply over international relief efforts in the famine-ravaged country.

It has emerged that aid officials have been aware for months that armed groups – most prominently Houthi rebels in the capital, Sana’a – have been diverting food aid into the key areas they control, including by manipulating data in malnutrition surveys used by the UN.

Officials concede that difficulties with access to many areas in Yemen under Houthi control, and aid agencies’ reliance on Houthi officials to collect much of the hunger data, have left them vulnerable to falsification.

Houthi officials have vociferously denied the allegations of food theft in Sana’a, disclosed on Monday. Aid workers who spoke to the Guardian anonymously in December detailed similar concerns about food diversion.

The allegations come in the midst of a fragile ceasefire between the Saudi-led coalition, which backs the official government, and Houthi rebels, in a conflict that has left 16 million people facing severe food insecurity. The World Food Programme is supplying about eight million of them with monthly aid.

The latest claims go a long way towards explaining the stark disparities in the UN’s official famine data for Yemen in comparison to assessments provided by other international aid groups, which have been warning of a much more serious crisis facing the country.

Following an investigation by the Associated Press, the admission by the World Food Programme this week that food aid was being stolen has led to the UN food agency admitting that in other areas hungry people “had been denied full rations”.

In a statement, the UN agency said: “The misappropriation of food relief came to light in a WFP review conducted during recent months. It was prompted by an increasing number of reports of humanitarian food for sale on the open market in the capital. What the checks unearthed was fraud being perpetrated by at least one local partner organisation tasked by WFP with handling and distributing its food assistance.”

David Beasley, WFP’s executive director, said: “At a time when children are dying in Yemen because they haven’t enough food to eat, that is an outrage. This criminal behaviour must stop immediately.”

Even as the theft of food aid was being reported, other agencies operating in Yemen were warning privately that they believed a more widespread diversion of aid might be taking place, raising serious questions over the effectiveness and vulnerability of the UN’s famine early-warning mechanism known as the Integrated Phase Classification system [IPC].

One senior aid official told the Guardian they believed that the IPC itself could have been manipulated to the benefit of Houthi-controlled areas and to the detriment of starving civilians in other parts of the country.

Bassem Mohamed Hassan, two, one of Yemen’s starving children, is weighed at a hospital in Hajjah province, September 2018. Photograph: Essa Ahmed/AFP/Getty Images

The official, who did not want to be named, said: “The reason I don’t believe the IPC figures is because they have been manipulated by political parties. And we have been a party to it. The [food security] surveys have been limited or only done by certain entities.

“If you look at the data, we have certain governorates [administrative divisions] that belong to a specific party to the conflict [that have the most need]. The data collection on acute malnutrition in Yemen is a disaster. Even if the UN agencies say it is under control, it is not.”

The scathing assessment follows repeatedly voiced concerns over the manipulation of food delivery to starving Yemenis by both of the main parties to the conflict.

Commenting on the latest claims of the diversion of food aid, a spokesman for WFP said: “So far, our monitoring has identified seven food distribution centres which we believe have been engaging in the misappropriation of our food stocks. These centres, located in Sana’a, are overseen by one of our local partner organisations affiliated with the Houthi administration in the capital.

“Our interviews with beneficiaries entitled to collect food from the seven centres indicated that nearly 60% of people had not received the assistance to which they were entitled.

“Records indicate that, during the months of August and September, about 1,200 metric tonnes of food were illicitly removed from storage and distributed or sold to people not entitled to receive the commodities. This amounts to about 1% of WFP food distributed per month nationwide.

“Other inquiries conducted by WFP in the Saada governorate showed only one-third of the intended ration was being provided to registered beneficiaries there.

“For now, we cannot confirm the exact amount of relief food that is being diverted in Yemen. Our monitoring – by WFP personnel and by third-party monitors – is as rigorous as possible in the circumstances, but we have not been permitted to implement an accountable beneficiary selection process in Houthi-controlled areas.”